source: trunk @ 6627

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Diff Rev Age Author Log Message
(edit) @6627   10 years melissa Switched TiffParser logging from 'debug' to 'trace'; see #512.
(edit) @6625   10 years curtis Fix autoscaling problem with >8-bit CompositeImages.
(edit) @6624   10 years curtis Remove obsolete constant from bf-cpp conflicts list.
(edit) @6623   10 years bdezonia make flesh for the color tests. remove unfinished tests. comment out some …
(edit) @6622   10 years melissa Ensure that xmlns:ome elements are preserved during transformation.
(edit) @6621   10 years melissa Merged r6614 and r6615 into trunk.
(edit) @6620   10 years bdezonia some work on composite testing and some code on dimension swapping tests. …
(edit) @6619   10 years melissa Updated stylesheets to  ome-xml:r645.
(edit) @6618   10 years callan Restoring MIAS reader overlay support.
(edit) @6617   10 years callan Support for TagAnnotation and TermAnnotation conversion.
(edit) @6616   10 years callan Re-run of code generation; support for mask bin data. ( ome-xml:r644)
(edit) @6612   10 years melissa Fixed parsing of large OME-XML files and pre-2010-04 files with …
(edit) @6610   10 years curtis Change default stack order to XYCZT, to match Hyperstack view option.
(edit) @6609   10 years curtis Fix bug in 'Metadata only' stack view option.
(edit) @6607   10 years curtis Fix plane ordering bug with channel separator when effectiveSizeC>1, …
(edit) @6606   10 years curtis Fix bug with fake data generation when rgbChannelCount>1.
(edit) @6604   10 years curtis Readd "Standard ImageJ" stack view option. Note that non-hyperstacks …
(edit) @6603   10 years curtis Cosmetic tweaks.
(edit) @6602   10 years melissa Throw a nicer exception if LuraWaveServiceImpl is instantiated with …
(edit) @6601   10 years melissa Added 'unknown' domain and updated various readers to use the unknown …
(edit) @6600   10 years melissa Fixed and uncommented most of the AnnotationRef conversion logic (and a …
(edit) @6598   10 years curtis Preserve channel-specific LUTs. Fixes #495 (again).
(edit) @6597   10 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6595   10 years curtis Better error handling when reading thumbnails.
(edit) @6594   10 years bdezonia put most all virtual subcases in place
(edit) @6592   10 years curtis Update required ImageJ version to 1.42+, due to CompositeImage.setLUTs …
(edit) @6591   10 years bdezonia more virtual test code
(edit) @6590   10 years bdezonia Added some virtual testing methods
(edit) @6588   10 years curtis Update copyright notice for LOCI plugins.
(edit) @6587   10 years bdezonia modified comboConcatSplit methods to work with BF's latest changes
(edit) @6585   10 years curtis Update component version numbers from 4.1.1 to 4.2-DEV.
(edit) @6583   10 years curtis Populate version information from Git, where applicable.
(edit) @6582   10 years callan Re-run of code generation; fixes UUID population in OMEXMLMetadataImpl. …
(edit) @6581   10 years curtis Preserve dimensional extents on concatenation.
(edit) @6580   10 years curtis Update color mode documentation a bit.
(edit) @6579   10 years bdezonia more options.setVirtual() support
(edit) @6578   10 years bdezonia started adding code to test everything with VirtualStacks also
(edit) @6576   10 years melissa Added experimental support for an alternate JPEG-2000 compression code.
(edit) @6575   10 years curtis Disable calibration function for INT32, since FloatProcessor is used. Also …
(edit) @6574   10 years bdezonia minor edits. enabled openAllSeries with concatenate in the combo tests.
(edit) @6573   10 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6572   10 years bdezonia Fixed the two split timepoints tests to match against modified CZT order
(edit) @6571   10 years curtis Fix indexing bug when reading only a subset of planes.
(edit) @6570   10 years curtis Minor tweaks.
(edit) @6569   10 years melissa Updated C++ headers to reflect changes to ome.xml.* in r6531.
(edit) @6568   10 years melissa Various fixes to OME-XML/OME-TIFF handling, including support for …
(edit) @6567   10 years melissa Fixed how pixels files are found, so that having multiple *.vws files in …
(edit) @6566   10 years melissa Tweaked pixel block detection to work with Slidebook 5.0.0.5 files.
(edit) @6565   10 years callan Fixing constructor of OMEXMLMetadataImpl
(edit) @6563   10 years curtis Remove debugging statement.
(edit) @6561   10 years curtis Do not fill indices for true color data if LUT is compatible with ImageJ.
(edit) @6560   10 years curtis Add a TODO note about discontinuous 16-bit LUT resampling.
(edit) @6558   10 years curtis Use composite mode by default for formerly-indexed images.
(edit) @6556   10 years curtis Fix problem with signed LUT indices.
(edit) @6554   10 years curtis Progress on proper handling of color modes.
(edit) @6553   10 years melissa Fixed a handful of core metadata and pixels offset bugs in Visitech …
(edit) @6552   10 years bdezonia minor edits
(edit) @6551   10 years callan Updating stylesheets. ( ome-xml:r640)
(edit) @6550   10 years callan Fixing enumeration handler logging when the requested value is null.
(edit) @6549   10 years callan More verbose tracing to track problems with stylesheet transforms.
(edit) @6548   10 years callan Moving transformed XML logging dump to the TRACE level.
(edit) @6547   10 years callan Make sure 2010-04-to-2010-06.xsl makes it into bio-formats.jar
(edit) @6546   10 years melissa Fixed compile errors introduced in r6531.
(edit) @6545   10 years curtis For indexed color fake data, return a different LUT for each channel.
(edit) @6544   10 years melissa Reverting r6536, as r6543 fixes the underlying problems in ListAnnotation.
(edit) @6543   10 years callan Re-run of code generation; superclass reference support. Added test case …
(edit) @6542   10 years callan Adding Xalan and its serializer dependency JAR to the Eclipse CLASSPATH.
(edit) @6541   10 years bdezonia Improved falseColor support in getPixelValue().
(edit) @6540   10 years callan Support for 2010-06 schema translation.
(edit) @6539   10 years callan Fixing "External libraries" Eclipse project CLASSPATH.
(edit) @6538   10 years callan Updating stylesheets from  ome-xml:r635.
(edit) @6537   10 years bdezonia minor changes
(edit) @6536   10 years melissa Temporarily commented out ListAnnotationRef population.
(edit) @6535   10 years bdezonia refactoring
(edit) @6534   10 years melissa Fixed a few issues with 16-bit LUTs.
(edit) @6533   10 years bdezonia more refactoring
(edit) @6532   10 years bdezonia mostly refactoring
(edit) @6531   10 years callan Re-run of code generation; working copy schema. Huge merge. (See …
(edit) @6530   10 years bdezonia Further support for indexed data
(edit) @6529   10 years bdezonia testColorCompositeSubcases() implemented for nonindexed data
(edit) @6528   10 years bdezonia started work on testCompositeSubcases(). Began refactor for general …
(edit) @6527   10 years melissa Tweaked Metamorph reader's type detection so that TIFFs are not …
(edit) @6526   10 years melissa Fixed Detector indices so that Detectors are properly populated and linked …
(edit) @6522   10 years curtis Fix problem with Stack Slicer macro keys.
(edit) @6521   10 years curtis Use explicit version number for JUnit JAR.
(edit) @6520   10 years curtis Remove dependency on OME Notes, in favor of loci.formats.gui.XMLWindow. …
(edit) @6519   10 years bdezonia minor refactorings
(edit) @6518   10 years bdezonia further work on various methods
(edit) @6517   10 years melissa Fixed scan-deps.pl warnings.
(edit) @6516   10 years melissa Eliminated several deprecation warnings.
(edit) @6515   10 years melissa Allow Metamorph reader to pick up TIFF files.
(edit) @6514   10 years melissa Javadoc tweaks.
(edit) @6513   10 years bdezonia edits towards a general getColorTable() based testing method. Also enabled …
(edit) @6512   10 years melissa Fixed a couple of minor channel bugs. testColorizeSubcases should pass …
(edit) @6511   10 years bdezonia remove print statements to simplify debugging
(edit) @6510   10 years bdezonia further work related to testColorizedSubcases()
(edit) @6509   10 years melissa Adjust strip offsets if 32-bit signed values are being used in > 2 GB …
(edit) @6508   10 years melissa * Added basic TIFF tile export. Closes #413. * Throw an exception in …
(edit) @6507   10 years melissa Couple of minor reader fixes.
(edit) @6506   10 years melissa * Updated JUnit version so that ImageJ plugin tests compile. * Overrode …
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